This article presents the complex case study of an ancient skeleton presenting a maxillary supernumerary tooth (mesiodens). The skeleton was found in an archaeological site in the western part of Romania and was dated back to the Eneolithic period, some 5500 years ago. The aim of this article is to analyze the mesiodens and the jaws in light of current knowledge regarding anomalies of dental development of past and present-time populations. The cranial remains were investigated from an orthodontic perspective through inspection and cone beam computed tomography (CBCT) scan. The occlusion was analyzed according to Angle’s classification and observations were made regarding the presence of calculus, dental wear, presence of caries, bone loss and ante-mortem tooth loss. Observations were made regarding tooth dimensions and comparisons were made with modern population. In this specific case, the mesiodens caused minimum disruption within the upper dental arch and the occlusion. Additionally, it did not have any negative impact on the adjacent teeth or cause any other complication. Judging by the analysis of the jaws, the presence of the mesiodens had little impact on the overall oral health of the person. As suggested by other findings in the scientific literature, the mesiodens is an anomaly found throughout all historical periods, from the oldest archaeological sites to present day.